Pub Date : 2025-10-30DOI: 10.1016/j.ympev.2025.108487
Michelle P. Mercês , Hazel Byrne , Natalie Finnegan , Maria L. Harada , Fernanda P. Paim , Felipe E. Silva , Anita Stone , Marcela G.M. Lima , Anthony B. Rylands , José de Sousa e Silva Júnior , Jessica W. Lynch
Phylogenetic relationships among squirrel monkeys (genus Saimiri) are still poorly resolved. Morphology-based taxonomies range from two to 12 taxa, while molecular phylogenies have recovered up to 17 different lineages. The last species account lists 11 taxa: Saimiri boliviensis boliviensis, S. boliviensis peruviensis, S. vanzolinii, S. oerstedii oerstedii, S. oerstedii citrinellus, S. sciureus, S. collinsi, S. cassiquiarensis, S. albigena, S. macrodon and S. ustus. Here we gathered a phylogenomic dataset for Saimiri using double digest restriction-site associated DNA sequencing (ddRadseq) to construct a phylogeny for squirrel monkeys in Amazonia. All the phylogenomic analyses strongly supported the division of the genus in two main clades, corresponding to the Gothic- and Roman-arch groups based on morphology, and provided strong support for five major lineages: S. boliviensis + S. vanzolinii; S. ustus; S. cassiquiariensis; S. macrodon; and S. sciureus + S. collinsi. Structure analyses showed evidence for population clusters based on geography within these lineages, but also shared ancestry across clusters, and Dsuite analyses showed evidence for gene flow across the Gothic species. Our time-calibrated tree confirmed that the diversification of Amazonian Saimiri occurred during the Pleistocene.
{"title":"Phylogenomics of Amazonian squirrel monkeys (Saimiri: Primates, Cebidae)","authors":"Michelle P. Mercês , Hazel Byrne , Natalie Finnegan , Maria L. Harada , Fernanda P. Paim , Felipe E. Silva , Anita Stone , Marcela G.M. Lima , Anthony B. Rylands , José de Sousa e Silva Júnior , Jessica W. Lynch","doi":"10.1016/j.ympev.2025.108487","DOIUrl":"10.1016/j.ympev.2025.108487","url":null,"abstract":"<div><div>Phylogenetic relationships among squirrel monkeys (genus <em>Saimiri</em>) are still poorly resolved. Morphology-based taxonomies range from two to 12 taxa, while molecular phylogenies have recovered up to 17 different lineages. The last species account lists 11 taxa: <em>Saimiri boliviensis boliviensis</em>, <em>S. boliviensis peruviensis</em>, <em>S. vanzolinii</em>, <em>S. oerstedii oerstedii</em>, <em>S. oerstedii citrinellus</em>, <em>S. sciureus</em>, <em>S. collinsi</em>, <em>S. cassiquiarensis, S. albigena</em>, <em>S. macrodon</em> and <em>S. ustus</em>. Here we gathered a phylogenomic dataset for <em>Saimiri</em> using <em>double digest</em> restriction-site associated DNA sequencing (ddRadseq) to construct a phylogeny for squirrel monkeys in Amazonia. All the phylogenomic analyses strongly supported the division of the genus in two main clades, corresponding to the Gothic- and Roman-arch groups based on morphology, and provided strong support for five major lineages: <em>S. boliviensis</em> + <em>S. vanzolinii</em>; <em>S. ustus</em>; <em>S. cassiquiariensis</em>; <em>S. macrodon</em>; and <em>S. sciureus</em> + <em>S. collinsi</em>. Structure analyses showed evidence for population clusters based on geography within these lineages, but also shared ancestry across clusters, and Dsuite analyses showed evidence for gene flow across the Gothic species. Our time-calibrated tree confirmed that the diversification of Amazonian <em>Saimiri</em> occurred during the Pleistocene.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108487"},"PeriodicalIF":3.6,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145427274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-28DOI: 10.1016/j.ympev.2025.108486
Shiyu Du , Feng Zhang
Insect genomes are largely composed of non-coding repetitive sequences, often exceeding 50 % of the total genomic content; these are also known as transposable elements (TEs). The increasing availability of extensive insect genomes, facilitated by advancements in sequencing technology, has made it feasible to explore the potential of TEs in insect systematics. Exhibiting varying degrees of differentiation across taxonomic levels, insect TEs may serve as informative characters for species-level analyses. This study focused on the Drosophiloidea as a case to evaluate the potential of TEs as phylogenetic markers and for insect phylogeny. We identified 2,390 species-specific TE families using genomes from 128 species and quantified their copy numbers in each species. Subsequently, we constructed phylogenetic trees based on the presence/absence (0/1 coding) of these TEs using Maximum Parsimony, Maximum Likelihood, and Bayesian Inference methods. Comparison with the recognized phylogeny showed incongruences in overall topology, especially at higher levels (suprageneric), where TE-based trees recovered about 51–55.8 % of nodes consistent with the phylogeny. At lower levels (infrageneric), TEs recovered monophyly in 54.5–68.2 % of nodes. Given the limitations of tree-based methods in resolving the relationships of species, we performed clustering analysis on normalized and dimensionally reduced TE copy numbers, which revealed that TEs can effectively distinguish closely related species. Furthermore, by considering the phylogenetic signal strength of TEs, we found that phylogenetic trees constructed using TEs with higher RI values (>0.5) exhibited the smallest normalized Robinson-Foulds distances to known phylogenies (0.379–0.408), indicating that accounting for phylogenetic signal may improve inference accuracy. Notably, we observed no significant difference (p-values = 0.7425) in the performance of TEs between genomes generated by next-generation and third-generation sequencing platforms. Clustering analysis of different TE types (including LTR, SINE, LINE, RC, DNA, and Unknown) indicated that all types provide comparable resolution for species delimitation. Overall, TEs show greater utility at lower taxonomic levels, particularly for species delimitation. This study provides insights into the use of genome-wide TE features for insect systematics, contributing to a better understanding of their application in phylogenetic and taxonomic studies.
{"title":"Harnessing transposable elements: A new frontier in insect systematics","authors":"Shiyu Du , Feng Zhang","doi":"10.1016/j.ympev.2025.108486","DOIUrl":"10.1016/j.ympev.2025.108486","url":null,"abstract":"<div><div>Insect genomes are largely composed of non-coding repetitive sequences, often exceeding 50 % of the total genomic content; these are also known as transposable elements (TEs). The increasing availability of extensive insect genomes, facilitated by advancements in sequencing technology, has made it feasible to explore the potential of TEs in insect systematics. Exhibiting varying degrees of differentiation across taxonomic levels, insect TEs may serve as informative characters for species-level analyses. This study focused on the Drosophiloidea as a case to evaluate the potential of TEs as phylogenetic markers and for insect phylogeny. We identified 2,390 species-specific TE families using genomes from 128 species and quantified their copy numbers in each species. Subsequently, we constructed phylogenetic trees based on the presence/absence (0/1 coding) of these TEs using Maximum Parsimony, Maximum Likelihood, and Bayesian Inference methods. Comparison with the recognized phylogeny showed incongruences in overall topology, especially at higher levels (suprageneric), where TE-based trees recovered about 51–55.8 % of nodes consistent with the phylogeny. At lower levels (infrageneric), TEs recovered monophyly in 54.5–68.2 % of nodes. Given the limitations of tree-based methods in resolving the relationships of species, we performed clustering analysis on normalized and dimensionally reduced TE copy numbers, which revealed that TEs can effectively distinguish closely related species. Furthermore, by considering the phylogenetic signal strength of TEs, we found that phylogenetic trees constructed using TEs with higher RI values (>0.5) exhibited the smallest normalized Robinson-Foulds distances to known phylogenies (0.379–0.408), indicating that accounting for phylogenetic signal may improve inference accuracy. Notably, we observed no significant difference (<em>p</em>-values = 0.7425) in the performance of TEs between genomes generated by next-generation and third-generation sequencing platforms. Clustering analysis of different TE types (including LTR, SINE, LINE, RC, DNA, and Unknown) indicated that all types provide comparable resolution for species delimitation. Overall, TEs show greater utility at lower taxonomic levels, particularly for species delimitation. This study provides insights into the use of genome-wide TE features for insect systematics, contributing to a better understanding of their application in phylogenetic and taxonomic studies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108486"},"PeriodicalIF":3.6,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145398587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-27DOI: 10.1016/j.ympev.2025.108488
Sergio D. Bolívar-Leguizamón , Aline Henrique Corrêa , Glayson Ariel Bencke , Luís F. Silveira
The identification of valid species is central to biology, and genetic data have been essential in uncovering new taxonomic units across groups. For polytypic taxa, genetics helps distinguish valid units from natural variation. Pulsatrix perspicillata (Spectacled Owl) is a widespread polytypic species with six recognized subspecies. We used genetic data and museomics techniques to: (i) test the validity of Strix pulsatrixWied, 1820 (=Pulsatrix perspicillata pulsatrix) as a species distinct from Pulsatrix perspicillata; and (ii) estimate the phylogenetic relationships and divergence times within the genus Pulsatrix Kaup, 1848. We conducted population structure and phylogenetic analyses using SNPs matrices and alignments of Ultraconserved Elements (UCEs) from 16 individuals of Pulsatrix spp., including four historical samples of P. p. pulsatrix. Additionally, we sequenced the mtDNA-ND2 gene from 38 samples representing all known Pulsatrix species to further elucidate phylogenetic relationships and estimate divergence times. Our results indicate that Pulsatrix perspicillata pulsatrix represents an independent lineage from P. perspicillata, as supported by its reciprocal monophyly and distinct population structure. UCE analyses also grouped P. koeniswaldiana (Tawny-browed Owl) and P. melanota (Band-bellied Owl) into a distinct cluster. Phylogenetic analyses based on both UCEs and mtDNA-ND2 sequences support the monophyly of the genus Pulsatrix. Pulsatrix koeniswaldiana and P. melanota form a monophyletic group that is sister to P. perspicillata. Pulsatrix diverged in the Late Miocene and diversified in the Pliocene-Quaternary. The evolutionary history of Pulsatrix appears to have been influenced by (a) the final phase of the Andean uplift and (b) climatic oscillations during the Pleistocene. Pulsatrix p. pulsatrix shows genetic divergence consistent with a species-level split from P. perspicillata, and we henceforth recognize it as Pulsatrix pulsatrix (Wied, 1820). We recommend future studies to assess its current distribution and inform the development of conservation strategies.
{"title":"Museomics resolves 200 years of taxonomic uncertainty: Strix pulsatrix Wied, 1820 (Strigiformes, Strigidae) is a valid species","authors":"Sergio D. Bolívar-Leguizamón , Aline Henrique Corrêa , Glayson Ariel Bencke , Luís F. Silveira","doi":"10.1016/j.ympev.2025.108488","DOIUrl":"10.1016/j.ympev.2025.108488","url":null,"abstract":"<div><div>The identification of valid species is central to biology, and genetic data have been essential in uncovering new taxonomic units across groups. For polytypic taxa, genetics helps distinguish valid units from natural variation. <em>Pulsatrix perspicillata</em> (Spectacled Owl) is a widespread polytypic species with six recognized subspecies. We used genetic data and museomics techniques to: (i) test the validity of <em>Strix pulsatrix</em> <span><span>Wied, 1820</span></span> (=<em>Pulsatrix perspicillata pulsatrix</em>) as a species distinct from <em>Pulsatrix perspicillata</em>; and (ii) estimate the phylogenetic relationships and divergence times within the genus <em>Pulsatrix</em> Kaup, 1848. We conducted population structure and phylogenetic analyses using SNPs matrices and alignments of Ultraconserved Elements (UCEs) from 16 individuals of <em>Pulsatrix</em> spp., including four historical samples of <em>P. p. pulsatrix</em>. Additionally, we sequenced the mtDNA-ND2 gene from 38 samples representing all known <em>Pulsatrix</em> species to further elucidate phylogenetic relationships and estimate divergence times. Our results indicate that <em>Pulsatrix perspicillata pulsatrix</em> represents an independent lineage from <em>P. perspicillata</em>, as supported by its reciprocal monophyly and distinct population structure. UCE analyses also grouped <em>P. koeniswaldiana</em> (Tawny-browed Owl) and <em>P. melanota</em> (Band-bellied Owl) into a distinct cluster. Phylogenetic analyses based on both UCEs and mtDNA-ND2 sequences support the monophyly of the genus <em>Pulsatrix</em>. <em>Pulsatrix koeniswaldiana</em> and <em>P. melanota</em> form a monophyletic group that is sister to <em>P. perspicillata</em>. <em>Pulsatrix</em> diverged in the Late Miocene and diversified in the Pliocene-Quaternary. The evolutionary history of <em>Pulsatrix</em> appears to have been influenced by (a) the final phase of the Andean uplift and (b) climatic oscillations during the Pleistocene. <em>Pulsatrix p. pulsatrix</em> shows genetic divergence consistent with a species-level split from <em>P. perspicillata</em>, and we henceforth recognize it as <em>Pulsatrix pulsatrix</em> (<span><span>Wied, 1820</span></span>). We recommend future studies to assess its current distribution and inform the development of conservation strategies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108488"},"PeriodicalIF":3.6,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145403004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-24DOI: 10.1016/j.ympev.2025.108484
Li-Sha Jiang , Yu Feng , Jun-Yi Zhang , Xiong Li , Min Liao , Heng-Ning Deng , Qi Yu , Bo Xu
The shrub genus Campylotropis (Fabaceae, trib. Desmodieae, subtrib. Lespedezinae) encompasses approximately 40 species, predominantly distributed across temperate and subtropical East Asia, with its diversity centered in the Hengduan Mountains and southern China. Historical constraints in sampling and methodological approaches have long obscured its evolutionary history and species relationships. This study provides the most comprehensive phylogenomic analysis of Campylotropis to date, incorporating 91 samples representing 40 taxa. Leveraging sequence data from 77 plastid genes and 1,233 single-copy nuclear genes (SCGs), we reconstructed the genus’s phylogenomic framework, estimated divergence times, inferred ancestral area distributions, and traced the evolution of key morphological traits. Our results robustly confirm the monophyly of Campylotropis, distinguishing it from allied genera. We delineated six well-supported clades within the genus and resolved previously unresolved relationships. The conflicts between nuclear and chloroplast phylogenies highlight a complex evolutionary history, likely influenced by chloroplast capture and incomplete lineage sorting (ILS) during rapid radiation. We found that global climate change and tectonic activities since the late Miocene likely shaped lineage diversification, with Quaternary climate oscillations potentially triggering rapid radiation within the genus. Ancestral area reconstruction suggests that Campylotropis originated in the Hengduan Mountains and southern China before dispersing swiftly across adjacent East Asian regions. By integrating extensive sampling with nuclear genomic data, this study elucidates the evolutionary history of Campylotropis and enhances our understanding of diversification processes in biodiversity hotspots.
{"title":"Phylogenomic framework, biogeography and character evolution of the genus Campylotropis (Fabaceae, Papilionoideae)","authors":"Li-Sha Jiang , Yu Feng , Jun-Yi Zhang , Xiong Li , Min Liao , Heng-Ning Deng , Qi Yu , Bo Xu","doi":"10.1016/j.ympev.2025.108484","DOIUrl":"10.1016/j.ympev.2025.108484","url":null,"abstract":"<div><div>The shrub genus <em>Campylotropis</em> (Fabaceae, trib. Desmodieae, subtrib. Lespedezinae) encompasses approximately 40 species, predominantly distributed across temperate and subtropical East Asia, with its diversity centered in the Hengduan Mountains and southern China. Historical constraints in sampling and methodological approaches have long obscured its evolutionary history and species relationships. This study provides the most comprehensive phylogenomic analysis of <em>Campylotropis</em> to date, incorporating 91 samples representing 40 taxa. Leveraging sequence data from 77 plastid genes and 1,233 single-copy nuclear genes (SCGs), we reconstructed the genus’s phylogenomic framework, estimated divergence times, inferred ancestral area distributions, and traced the evolution of key morphological traits. Our results robustly confirm the monophyly of <em>Campylotropis</em>, distinguishing it from allied genera. We delineated six well-supported clades within the genus and resolved previously unresolved relationships. The conflicts between nuclear and chloroplast phylogenies highlight a complex evolutionary history, likely influenced by chloroplast capture and incomplete lineage sorting (ILS) during rapid radiation. We found that global climate change and tectonic activities since the late Miocene likely shaped lineage diversification, with Quaternary climate oscillations potentially triggering rapid radiation within the genus. Ancestral area reconstruction suggests that <em>Campylotropis</em> originated in the Hengduan Mountains and southern China before dispersing swiftly across adjacent East Asian regions. By integrating extensive sampling with nuclear genomic data, this study elucidates the evolutionary history of <em>Campylotropis</em> and enhances our understanding of diversification processes in biodiversity hotspots.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108484"},"PeriodicalIF":3.6,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145416753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-22DOI: 10.1016/j.ympev.2025.108479
Jie Tang , Ying Jiang , Zhe Hu , Huizhen Zhou , Dawei You , Maurycy Daroch
{"title":"Corrigendum to “Genomic and phenotypic characterization of Thermosynechococcus-like strains reveals eight species within the genus Thermosynechococcus and a novel genus Parathermosynechococcus gen. nov.”. [Mol. Phylogenet. Evol. 197 (2024) 108094]","authors":"Jie Tang , Ying Jiang , Zhe Hu , Huizhen Zhou , Dawei You , Maurycy Daroch","doi":"10.1016/j.ympev.2025.108479","DOIUrl":"10.1016/j.ympev.2025.108479","url":null,"abstract":"","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108479"},"PeriodicalIF":3.6,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145356843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-17DOI: 10.1016/j.ympev.2025.108480
Pia Marinček , Jing Vir Leong , Loic Pittet , Ètienne Léveillé-Bourret , Tommi Nyman , Maria Tomoshevich , Evgeny Banaev , Li He , Elvira Hörandl , Martin Volf , Natascha D. Wagner
The spatio-temporal evolution of woody plant lineages in the Holarctic is still understudied, limiting our understanding of evolutionary processes that promote higher diversity at higher latitudes in some lineages, which contradicts the latitudinal gradient hypothesis which predicts higher species richness in the tropics. Shrub willows (Salix subgenus Vetrix) comprise about 350 species of which many are adapted to arctic-alpine ecosystems and thus form an important element across the Holarctic region. In this study, we utilized RAD sequencing to estimate the spatio-temporal evolution of the Vetrix clade based on about 140 species covering most of its morphological and geographical diversity. The resolved phylogeny revealed four lineages: the Pan-Himalayan clade, the North American clade and two clades containing species from Eurasia. Widespread circumpolar species form a hybridogenetic grade between the Eurasian and North American clades. Our results confirm that shrub willows originated in the Tertiary, probably in Asia, and that diversification coincided with the climatic cooling in the Pleistocene. At least two radiations were observed, in the Pan Himalayas and in North America. Speciation was further shaped by migration and dispersal in Eurasia, likely accelerated by the uplift of mountain chains, the closure of the Turgai Strait and expansion of suitable habitats. The dated phylogeny revealed that speciation of arctic lineages predates adaptation to high latitudes, as also evident from the fossil record. Small wind-dispersed seeds enabled shrub willows to colonize the expanding arctic tundra regions in the Miocene and their recolonization after the LGM. Given the high observed number of polyploid species equally distributed in all clades and indications of genetic admixture, we assume that species diversity in shrub willows was additionally increased by hybridization and polyploidization.
{"title":"Spatio-temporal evolution of shrub willows (Salix subgenus Vetrix clade) on a global scale","authors":"Pia Marinček , Jing Vir Leong , Loic Pittet , Ètienne Léveillé-Bourret , Tommi Nyman , Maria Tomoshevich , Evgeny Banaev , Li He , Elvira Hörandl , Martin Volf , Natascha D. Wagner","doi":"10.1016/j.ympev.2025.108480","DOIUrl":"10.1016/j.ympev.2025.108480","url":null,"abstract":"<div><div>The spatio-temporal evolution of woody plant lineages in the Holarctic is still understudied, limiting our understanding of evolutionary processes that promote higher diversity at higher latitudes in some lineages, which contradicts the latitudinal gradient hypothesis which predicts higher species richness in the tropics. Shrub willows (<em>Salix</em> subgenus <em>Vetrix</em>) comprise about 350 species of which many are adapted to arctic-alpine ecosystems and thus form an important element across the Holarctic region. In this study, we utilized RAD sequencing to estimate the spatio-temporal evolution of the <em>Vetrix</em> clade based on about 140 species covering most of its morphological and geographical diversity. The resolved phylogeny revealed four lineages: the Pan-Himalayan clade, the North American clade and two clades containing species from Eurasia. Widespread circumpolar species form a hybridogenetic grade between the Eurasian and North American clades. Our results confirm that shrub willows originated in the Tertiary, probably in Asia, and that diversification coincided with the climatic cooling in the Pleistocene. At least two radiations were observed, in the Pan Himalayas and in North America. Speciation was further shaped by migration and dispersal in Eurasia, likely accelerated by the uplift of mountain chains, the closure of the Turgai Strait and expansion of suitable habitats. The dated phylogeny revealed that speciation of arctic lineages predates adaptation to high latitudes, as also evident from the fossil record. Small wind-dispersed seeds enabled shrub willows to colonize the expanding arctic tundra regions in the Miocene and their recolonization after the LGM. Given the high observed number of polyploid species equally distributed in all clades and indications of genetic admixture, we assume that species diversity in shrub willows was additionally increased by hybridization and polyploidization.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108480"},"PeriodicalIF":3.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145330835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-17DOI: 10.1016/j.ympev.2025.108483
Xuan Pan , Buqing Peng , Xuming Wang , Zhongzheng Chen , Hao Cheng , Rui Liao , Chia-Lung Huang , Jiatang Li , Shaoying Liu
Species delimitation based on genetic data plays a critical role in taxonomy research, particularly for resolving taxonomically complex groups and detecting cryptic diversity. However, few studies have assessed the consistency and reliability of the various species delimitation approaches using the real dataset. In this study, we compared the most widely used approaches for species delimitation within the complex group of the Apodemus genus from China. Multiple species delimitation approaches were applied, including the multispecies coalescent model- and machine learning-based approaches. Unexpectedly, we observed considerable discrepancies across methods, with some results lacking taxonomic validity. To resolve the taxonomic puzzle of this taxon, we integrated phylogenetic and population analyses with morphological and ecological assessments, ultimately recognizing nine valid species and identifying one cryptic species. Phylogeographic analyses of endemic lineages in east Himalayan Mountains of Southwest China indicated that orogenic activity and glacial-interglacial cycles have played key roles in the speciation and diversification of Apodemus in China. These results highlight the challenges of species delimitation in taxonomically complex groups and demonstrate that relying solely on molecular methods is insufficient. We advocate an integrative taxonomic framework that combines molecular, morphological, and ecological data to address these taxonomic puzzles.
{"title":"Species delimitation within a taxonomically complex group: An example from the genus Apodemus (Rodentia: Muridae)","authors":"Xuan Pan , Buqing Peng , Xuming Wang , Zhongzheng Chen , Hao Cheng , Rui Liao , Chia-Lung Huang , Jiatang Li , Shaoying Liu","doi":"10.1016/j.ympev.2025.108483","DOIUrl":"10.1016/j.ympev.2025.108483","url":null,"abstract":"<div><div>Species delimitation based on genetic data plays a critical role in taxonomy research, particularly for resolving taxonomically complex groups and detecting cryptic diversity. However, few studies have assessed the consistency and reliability of the various species delimitation approaches using the real dataset. In this study, we compared the most widely used approaches for species delimitation within the complex group of the <em>Apodemus</em> genus from China. Multiple species delimitation approaches were applied, including the multispecies coalescent model- and machine learning-based approaches. Unexpectedly, we observed considerable discrepancies across methods, with some results lacking taxonomic validity. To resolve the taxonomic puzzle of this taxon, we integrated phylogenetic and population analyses with morphological and ecological assessments, ultimately recognizing nine valid species and identifying one cryptic species. Phylogeographic analyses of endemic lineages in east Himalayan Mountains of Southwest China indicated that orogenic activity and glacial-interglacial cycles have played key roles in the speciation and diversification of <em>Apodemus</em> in China. These results highlight the challenges of species delimitation in taxonomically complex groups and demonstrate that relying solely on molecular methods is insufficient. We advocate an integrative taxonomic framework that combines molecular, morphological, and ecological data to address these taxonomic puzzles.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108483"},"PeriodicalIF":3.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145330865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-16DOI: 10.1016/j.ympev.2025.108482
Edward A. Myers , Alexander D. McKelvy , Dirk J. Stevenson , Frank T. Burbrink
Understanding phylogeographic structure is a key step in examining the processes related to lineage divergence and speciation. It is often expected that wide-ranging taxa will be composed of deeply divergent lineages and that codistributed species will have similar population genetic structure. Within the southeastern coastal plain of North America, a biodiversity hotspot, the evolutionary processes that have led to the accumulation of diversity are underexplored. Several process within this region could be responsible for species diversification, including past changes in climate, fluctuating sea levels, and the formation of river systems. However, it is also possible that a pattern of isolation-by-distance can explain population genetic structure found in widely distributed species, which can serve as a null hypothesis for observed genetic structure. We generate a reduced representation genomic dataset with population level sampling for two sister species of snakes endemic to the southeastern coastal plain, the mudsnakes and rainbow snakes (Farancia abacura and F. erytrogramma, respectively). With these data we find a strong signal of population divergence in F. abacura, while isolation-by-distance alone explains genetic divergence in F. erytrogramma. We also identify several genomic regions associated with environmental variation that may be key to local adaptation. Lastly, we find that the best fit demographic model includes gene flow during the initial divergence of these two species. This model also suggests that there is current unidirectional gene flow from the eastern F. abacura lineage into F. erytrogramma. However, the two F. abacura lineages appear to be reproductively isolated. We suggest further comparative phylogeographic work to understand the full suite of evolutionary processes driving diversification and endemism in the southeastern coastal plain.
{"title":"Pleistocene speciation and isolation-by-distance within North American mud and rainbow snakes","authors":"Edward A. Myers , Alexander D. McKelvy , Dirk J. Stevenson , Frank T. Burbrink","doi":"10.1016/j.ympev.2025.108482","DOIUrl":"10.1016/j.ympev.2025.108482","url":null,"abstract":"<div><div>Understanding phylogeographic structure is a key step in examining the processes related to lineage divergence and speciation. It is often expected that wide-ranging taxa will be composed of deeply divergent lineages and that codistributed species will have similar population genetic structure. Within the southeastern coastal plain of North America, a biodiversity hotspot, the evolutionary processes that have led to the accumulation of diversity are underexplored. Several process within this region could be responsible for species diversification, including past changes in climate, fluctuating sea levels, and the formation of river systems. However, it is also possible that a pattern of isolation-by-distance can explain population genetic structure found in widely distributed species, which can serve as a null hypothesis for observed genetic structure. We generate a reduced representation genomic dataset with population level sampling for two sister species of snakes endemic to the southeastern coastal plain, the mudsnakes and rainbow snakes (<em>Farancia abacura</em> and <em>F. erytrogramma</em>, respectively). With these data we find a strong signal of population divergence in <em>F. abacura</em>, while isolation-by-distance alone explains genetic divergence in <em>F. erytrogramma</em>. We also identify several genomic regions associated with environmental variation that may be key to local adaptation. Lastly, we find that the best fit demographic model includes gene flow during the initial divergence of these two species. This model also suggests that there is current unidirectional gene flow from the eastern <em>F. abacura</em> lineage into <em>F. erytrogramma</em>. However, the two <em>F. abacura</em> lineages appear to be reproductively isolated. We suggest further comparative phylogeographic work to understand the full suite of evolutionary processes driving diversification and endemism in the southeastern coastal plain.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108482"},"PeriodicalIF":3.6,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-15DOI: 10.1016/j.ympev.2025.108481
Richard Bačák , Marek Šlenker , Barbora Šingliarová , Terezie Mandáková , Katarína Skokanová , Ingrid Turisová , Peter Turis , Janka Smatanová , Judita Zozomová-Lihová
Accurate species delimitation is essential for understanding biodiversity and evolutionary processes, yet it remains challenging in taxonomically complex groups shaped by recent divergence and reticulate evolution. Nevertheless, such groups offer unique insights into the earliest stages of speciation and its driving forces. The genus Erysimum (Brassicaceae), notable for its karyological diversity and high endemism, represents an excellent model for such studies. Here, we investigated the E. odoratum complex, encompassing up to 10 recognized species in the Carpathians and western Balkans, to test its monophyletic origin, clarify species boundaries and elucidate the main drivers of diversification. We combined cytotype screening (chromosome counting and flow cytometry), morphometric analysis, and two high-throughput sequencing methods: RADseq, to resolve phylogenetic relationships as well as to detect fine-scale genetic structure and introgression; and target enrichment (Hyb-Seq), to elucidate polyploid origins. Our results demonstrate that the studied complex is polyphyletic, and we focused on the lineage comprising E. odoratum s.str. and Carpathian species. Phylogenomic data from the Carpathians contradict traditional taxonomy, which recognized up to four diploid endemics, and instead support a single species, E. witmannii with geographically structured genetic variation. Within E. odoratum s.str., we identified multiple polyploid cytotypes resulting from independent auto- and allopolyploidization events, although disentangling parental subgenomes, ancestral polymorphisms, and introgression remains difficult. We propose that diversification in this species complex has been driven by a combination of allopatric divergence and reticulate evolution (involving both introgression and allopolyploidy), further shaped by chromosomal dynamics such as dysploidy.
{"title":"Understanding early stages of speciation: Allopatric divergence, introgression and chromosomal dynamics in the Erysimum odoratum species complex","authors":"Richard Bačák , Marek Šlenker , Barbora Šingliarová , Terezie Mandáková , Katarína Skokanová , Ingrid Turisová , Peter Turis , Janka Smatanová , Judita Zozomová-Lihová","doi":"10.1016/j.ympev.2025.108481","DOIUrl":"10.1016/j.ympev.2025.108481","url":null,"abstract":"<div><div>Accurate species delimitation is essential for understanding biodiversity and evolutionary processes, yet it remains challenging in taxonomically complex groups shaped by recent divergence and reticulate evolution. Nevertheless, such groups offer unique insights into the earliest stages of speciation and its driving forces. The genus <em>Erysimum</em> (Brassicaceae), notable for its karyological diversity and high endemism, represents an excellent model for such studies. Here, we investigated the <em>E. odoratum</em> complex, encompassing up to 10 recognized species in the Carpathians and western Balkans, to test its monophyletic origin, clarify species boundaries and elucidate the main drivers of diversification. We combined cytotype screening (chromosome counting and flow cytometry), morphometric analysis, and two high-throughput sequencing methods: RADseq, to resolve phylogenetic relationships as well as to detect fine-scale genetic structure and introgression; and target enrichment (Hyb-Seq), to elucidate polyploid origins. Our results demonstrate that the studied complex is polyphyletic, and we focused on the lineage comprising <em>E. odoratum</em> s.str. and Carpathian species. Phylogenomic data from the Carpathians contradict traditional taxonomy, which recognized up to four diploid endemics, and instead support a single species, <em>E. witmannii</em> with geographically structured genetic variation. Within <em>E. odoratum</em> s.str., we identified multiple polyploid cytotypes resulting from independent auto- and allopolyploidization events, although disentangling parental subgenomes, ancestral polymorphisms, and introgression remains difficult. We propose that diversification in this species complex has been driven by a combination of allopatric divergence and reticulate evolution (involving both introgression and allopolyploidy), further shaped by chromosomal dynamics such as dysploidy.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108481"},"PeriodicalIF":3.6,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-07DOI: 10.1016/j.ympev.2025.108475
Xiao-Dong Xu , Chen-Yang Shen , Kenneth B. Storey , Dan-Na Yu , Yue Ma , Jia-Yong Zhang
The evolutionary relationships within the mantid subfamily Hierodulinae remain contentious, particularly concerning the morphological diversity and classification of species with leaf-like pronotum, which are broad and flattened thoracic structures. Traditionally regarded as a defining characteristic of the genus Rhombodera, specifically as a specialized pronotal trait, mitochondrial phylogenomics has cast doubt on this assumption, suggesting potential homoplasy. In this study, we generated 30 high-quality transcriptomes of Hierodulinae and established the first Mantodea-specific orthologous database (Mantodea_odb) to identify universal single-copy orthologues (USCOs) for phylogenomic inference. By integrating genomic and transcriptomic data, we reconstructed well-supported phylogenetic trees using both maximum likelihood and coalescent-based approaches, which provided the framework to assess evolutionary patterns of morphological traits. Divergence time estimation and ancestral state reconstruction suggested that the leaf-like pronotum evolved independently on multiple occasions within Hierodulinae, corresponding temporally to the late Paleogene to early Neogene (Oligocene-Miocene transition, ca. 20–23 Ma). Notably, our molecular phylogeny exhibits a strong correlation with distinct clades delineated by male genital morphology, thereby resolving longstanding taxonomic inconsistencies. These findings reveal decoupled evolutionary patterns between homoplastic pronotal traits and conserved genital morphology in Hierodulinae, showcasing how phylogenomics can discriminate between convergent and conserved traits.
{"title":"Phylogenomics insights into the evolution of pronotal leaf mimicry in Hierodulinae (Mantodea: Mantidae)","authors":"Xiao-Dong Xu , Chen-Yang Shen , Kenneth B. Storey , Dan-Na Yu , Yue Ma , Jia-Yong Zhang","doi":"10.1016/j.ympev.2025.108475","DOIUrl":"10.1016/j.ympev.2025.108475","url":null,"abstract":"<div><div>The evolutionary relationships within the mantid subfamily Hierodulinae remain contentious, particularly concerning the morphological diversity and classification of species with leaf-like pronotum, which are broad and flattened thoracic structures. Traditionally regarded as a defining characteristic of the genus <em>Rhombodera</em>, specifically as a specialized pronotal trait, mitochondrial phylogenomics has cast doubt on this assumption, suggesting potential homoplasy. In this study, we generated 30 high-quality transcriptomes of Hierodulinae and established the first Mantodea-specific orthologous database (Mantodea_odb) to identify universal single-copy orthologues (USCOs) for phylogenomic inference. By integrating genomic and transcriptomic data, we reconstructed well-supported phylogenetic trees using both maximum likelihood and coalescent-based approaches, which provided the framework to assess evolutionary patterns of morphological traits. Divergence time estimation and ancestral state reconstruction suggested that the leaf-like pronotum evolved independently on multiple occasions within Hierodulinae, corresponding temporally to the late Paleogene to early Neogene (Oligocene-Miocene transition, ca. 20–23 Ma). Notably, our molecular phylogeny exhibits a strong correlation with distinct clades delineated by male genital morphology, thereby resolving longstanding taxonomic inconsistencies. These findings reveal decoupled evolutionary patterns between homoplastic pronotal traits and conserved genital morphology in Hierodulinae, showcasing how phylogenomics can discriminate between convergent and conserved traits.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108475"},"PeriodicalIF":3.6,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145253892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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